Darryl Holman
117 Denny Hall
206-543-7586
djholman@u.washington.edu
Course web page: http://faculty.washington.edu/~djholman/bioa482
Autumn 2003
Scope: This course surveys population genetics theory as applied to studies of micro-evolutionary changes in human populations. We will look at the effects of mutation, selection, inbreeding, gene flow, and genetic drift on changes in allele frequency in human populations. During the last week of class we will also spend some time studying quantitative genetics. Much of the course is about formal (i.e. mathematical) models for changes in allele frequencies (or phenotypes) over time. An additional focus is the ways in which genetic variability has been used to study affinities among different groups of people and reconstruct the past dynamics human populations.
Objective: The objectives of this course are to: (1) provide you with a solid foundation for understanding the genetic basis of evolution; (2) provide you with tools, concepts, and ways of thinking about quantitative problems in biological anthropology and evolutionary biology; (3) provide sufficient historical, intellectual, and mathematical background so that you can evaluate contemporary research in anthropological genetics.
Classes: MWF, 2:30-3:50 pm in 217 Denny Hall. The final exam is scheduled for 2:30-4:20 pm, Monday, Dec. 15, 2003, 217 Denny Hall.
Office hours: I will usually be available after class for office hours. Other times can be arranged. Feel free to use email (at the address listed above) to contact me with questions or to set up an appointment.
Textbook and readings: The text for this course is Hartl and Clark, Principles of Population Genetics, 3rd edition, 1997 published by Sinauer Associates, Inc. Be certain you get the third edition of this book as it differs substantially from previous editions. The textbook is oriented toward general population genetics rather than human population genetics. Additional readings on topics of interest to anthropologists will supplement the text. These readings will serve as illustrations of the principles discussed in lecture and the text, and will also be used as the basis for some class discussions. Please try to have weekly readings done before you come to class on Wednesday.
Grades: You will be evaluated on 7 problem sets that will make up 60% of your final grade, one midterm exam (15%), and a cumulative final exam (20%). Additionally, 5% of your grade will be based on your participation in a class debate on the origins of modern Homo sapiens (discussed below).
Problem sets: Short problem sets will be assigned most weeks. Each problem set is worth about 8.6% of your final grade. The problems will be based on lecture material, textbook readings, and paper readings. Problem sets will be made up of both analytical problems and short written answers. I encourage you to work in groups. If so, use the opportunity to ensure a complete understanding of the problems—you will see similar problems on the exams. You may use any references (other books, readings, web pages) to work on the problems. For some problems will want to use a computer spreadsheet. When time permits, we will end class a few minutes early on Friday so that people can work in groups on problem sets. Typically, problem sets will be oriented toward solving numerical problems and interpreting the results. The problems at the end of each chapter are good examples of the types of problems you will receive for homework and on exams.
Problem sets will be handed out on Friday (usually) and are due at the start of class on the following Wednesday unless otherwise noted in the syllabus.
In part, the problem sets test your ability to do the work under time constraints. Therefore, the grade of a late problem set will depreciate by 10% per day, including any fraction of a day late. For example, if you would have gotten a 95% on the problem set, it would depreciate to 85.5% for being one day late, 77% by for 2 days late, 69% for day 3 and so on.
Exam: Two exams will be given in the course: a midterm and a final exam. The midterm will make up 15% of your grade and the final exam will make up 20% of your grade. Each exam will have two parts. The first part will be short essay questions covering concepts and ideas. The second part will be problems similar to those on the problem sets. The final exam will cover material from the entire course. Exams will be closed-book. However, you will be allowed to make up one sheet of notes (double sided) for use during the exam.
The debate: Anthropologists are deeply divided over the timing of and demographic processes associated with the origin of modern Homo sapiens. For the last 15 years, genetic evidence has increasingly played a role in the debate. We will hold a debate on this topic, with an emphasis on the genetic evidence for each side in the debate. You can choose which side of the debate you wish to support. Each side will work as a group to make up and present their case. On Wed, Dec 3, we will begin two days of debate and discussion.
The format will be as follows: the Multiregional group will begin with a 20 minute group presentation for their side of the debate. This will be followed by 20 minutes by the Recent African Origins group. The rest of the class will be an open discussion. On Friday, there will be 20 minutes rebuttals on each side (informed by the previous day’s discussion). The remainder of the class will be a discussion with emphasis on ways of scientifically testing each of the theories using the tools of population genetics. Each team will turn in a bibliography of reading materials they consulted in their research.
Topics: Course stuff. Theoretical & empirical aims. Some background. Models and the scientific method. Probability. Estimation.
Readings: Hartl and Clark Chapter 1.
Problem set 1 distributed (Friday)
Topics: Phenotypic variation. Measuring genetic variation. Polymorphism.
Readings: Hartl and Clark Chapter 2
Problem set 1 due (Wednesday). Problem set 2 distributed (Friday).
Topics: Random mating. Hardy Weinberg. Linkage disequilibrium.
Note: Dr. Steve Goodreau will give a guest lecture on Friday, Oct 17th.
Readings:
Hartl and Clark Chapter 3
Lindahl T (1997) Facts and artifacts of ancient DNA Cell 90:1-3.
Kahn P, Gibbons A (1997) DNA from an extinct human. Science 277:176-178.
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19-30.
Problem set 2 due (Wednesday). Problem set 3 distributed (Friday).
Topics: Heterozygosity. population subdivision. Inbreeding. Assortative mating.
Readings:
Hartl and Clark Chapter 4
Trost C (1982) The blue people of Troublesome Creek. Science 82. Washington D.C.: American Academy for the Advancement of Science. pp. 35-9.
Bamshad MJ, Watkins WS, Dixon ME, Jorde LB, Rao BB, Naidu JM, Ravi Prasad BV, Rasanayagam A, Hammer MF (1998) Female gene flow stratifies Hindu castes. Nature 395:651-2.
Problem set 3 due (Wednesday). Problem set 4 distributed (Friday).
Topics: Mutation. Recombination. Migration.
Readings:
Hartl and Clark Chapter 5
Kaessmann H, Wiebe V, Pääbo S (1999) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286:1159-1162.
Problem set 4 due (Wednesday).
Topics: Single locus model. Fisher's Fundamental theorem of natural selection. Selection-mutation balance. Two locus model.
Readings:
Hartl and Clark Chapter 6
Neel JV (1958) The study of natural selection in primitive and civilized human populations. Human Biology 30(1):43-72.
Neel JV (1990) Update to "The study of natural selection in primitive and civilized human populations. Human Biology 61(5-6):811-23.
In-Class Midterm Exam: Wed, Nov 9.
Topics: Multiple locus model. Molecular level. Kin selection. Sexual selection.
Readings:
Luzzatto L and Notaro R (2001) Protecting against bad air. Science 293:442-3.
Tishkof SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, Destro-Bisol G, Drousiotou A, Dangerfield B, Lefranc G, Loiselet J, Piro A, Stoneking M, Tagarelli A, Tagarelli G, Touma EH, Willimas SM, Clark AG (2001) Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293:455-62.
Problem set 5 distributed (Wednesday).
Topics: The statistics of drift. Diffusion models. Effective population size. Mutation-drift balance. Infinite alleles model. Infinite sites models.
Readings:
Hartl and Clark Chapter 7
Wright S(1988) Surfaces of selective value revisited. The American Naturalist 131:115-23.
Problem set 5 due (Wednesday). Problem set 6 distributed (Wednesday).
Topics: The neutral theory. The molecular clock. Molecular phylognetics.
Readings: Hartl and Clark Chapter 8
Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325(6099):31-6.
Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR and Sherry ST (1998) Genetic traces of ancient demography. Proceedings of the National Academy of Sciences 95:1961-7.
Problem set 6 due (Wednesday). Problem set 7 distributed (Wednesday).
Readings: Hartl and Clark Chapter 8
Templeton AR (1999) Human races: A genetic and evolutionary perspective. American Anthropologist 100(3):632-50.
Takahata N, Lee S-H, Satta Y (2001) Testing multiregionality of Modern Human Origins. Molecular Biology and Evolution 18:172-83.
Note: Wednesday and Friday class sessions will be devoted to a debate on the major theories of the origin of Modern Homo sapiens.
Problem set 7 due (Friday).
Topics: Quantitative traits. Evolution of quantitative traits.
Hartl and Clark Chapter 10
Beall CM, Strohl KP, Blangero J, Williams-Blangero S, Decker MJ, Brittenham GM, Goldstein MC (1997). Quantitative genetic analysis of arterial oxygen saturation in Tibetan highlanders. Human Biology 69(5):597-604.